README.md

Single

Single is an easy-to-use single-molecule imaging program!

Single allows to control unlimited number of shutters, also supports N-color alternate excitation(ALEX), automatic focusing, and automatic flow features.

Single is written in C#, and completely free to use.

Single is currently being used at:

• Single Molecule Biophysics Laboratory, Seoul National University
• Center for Theragnosis, Korea Institute of Science and Technology
• Nano-bio Photonics Division, Advanced Phothonics Research Institute (of Gwangju Institute of Science and Technology)
• Nanobio Imaging Laboratory, Gwangju Institute of Science and Technology
• Molecular Genome Engineering Laboratory, Hanyang University
• Bio-nanoscopy Laboratory, Seoul National University
• Single Molecule Cellular Biology Laboratory, Seoul National University
• Biophysical Laboratory, Chung-Ang University

Compatible Hardwares

1. Basic Imaging / ALEX

   • Any Andor EMCCD.
   • National Instruments(NI) Counterboards. Currently the program has been only tested with NI PCI-6601/2 (http://sine.ni.com/nips/cds/view/p/lang/en/nid/211875), however, any NI counterboards should also work. For your information, PCI-6601 supports only 3 counters so you will need PCI-6602 (or above) if you want 4-color ALEX.
   • Any electronic shutters compatible with the counterboards. For ALEX FRET imaging, we have used VS35 series from Uniblitz (VS35S2T1-24).

2. Automatic Focusing

   • Z-axis stages. Currently, ASI (Applied Scientific Instrumentation) MS-2000 control unit, MCL (Mad City Labs) C-Focus, and PI (Physik Instrumente) E-516 control unit are supported.
   • Additionally a cylinderical lens is required for this feature. Please refer to the following article for more information (and please cite if you use it): Hwang, W. et al. Autofocusing system based on optical astigmatism analysis of single-molecule images, Opt. Express 2012, 20 (28), 29353-29360.

3. Automatic Pump Control

   • Any Chemyx Fusion series syringe pumps.
   • Harvard PHD 2000 syringe pump.

Prerequisites

1. Auto-focusing and Auto flow runs in seperate threads, so CPU with quad core or more cores is recommended. Also vertical screen resolution should be more than 1050 pixels in order to display settings panel properly.
2. NI DAQmx. Download it here: http://www.ni.com/download/ni-daqmx-14.1/4953/en/
3. All other required device drivers (EMCCD, counterboards, Z-axis stages, etc.). Note that DLL for Andor CCD (atmcd32cs.dll and atmcd32d.dll), PI GCS2 piezo stage (E7XX_GCS2_DLL.dll), and for Mad City Labs' C-Focus (Madlib.dll) is already included with the distribution; you can exchange one of the dlls to the one working with your setup.
4. DotNet framework 4.5 (or above). If you have Visual Studio 2013 or above, then you can skip it. DotNet framework is also installable via Setup.exe.

Installation

1. Download Binary distribition here: https://github.com/pjb7687/single/releases/download/v1.0.4/Singlev1.0.4-Setup.exe or Build your own binary from source code.
2. Download and install all prerequisites. See above section.
3. Run Single.
4. In Settings tab, set all values according to your setup.

License

Copyright (c) 2013, Jeongbin Park All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.